6EPY

Structure of the PBP MelB (Atu4661) in complex with raffinose from A.fabrum C58


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogenAgrobacterium fabrum.

Meyer, T.Vigouroux, A.Aumont-Nicaise, M.Comte, G.Vial, L.Lavire, C.Morera, S.

(2018) J Biol Chem 293: 7930-7941

  • DOI: https://doi.org/10.1074/jbc.RA118.001856
  • Primary Citation of Related Structures:  
    6EPY, 6EPZ, 6EQ0, 6EQ1, 6EQ8

  • PubMed Abstract: 

    The bacterial plant pathogen Agrobacterium fabrum uses periplasmic-binding proteins (PBPs) along with ABC transporters to import a wide variety of plant molecules as nutrients. Nonetheless, how A. fabrum acquires plant metabolites is incompletely understood. Using genetic approaches and affinity measurements, we identified here the PBP MelB and its transporter as being responsible for the uptake of the raffinose family of oligosaccharides (RFO), which are the most widespread d-galactose-containing oligosaccharides in higher plants. We also found that the RFO precursor galactinol, recently described as a plant defense molecule, is imported into Agrobacterium via MelB with nanomolar range affinity. Structural analyses and binding mode comparisons of the X-ray structures of MelB in complex with raffinose, stachyose, galactinol, galactose, and melibiose (a raffinose degradation product) revealed how MelB recognizes the nonreducing end galactose common to all these ligands and that MelB has a strong preference for a two-unit sugar ligand. Of note, MelB conferred a competitive advantage to A. fabrum in colonizing the rhizosphere of tomato plants. Our integrative work highlights the structural and functional characteristics of melibiose and galactinol assimilation by A. fabrum , leading to a competitive advantage for these bacteria in the rhizosphere. We propose that the PBP MelB, which is highly conserved among both symbionts and pathogens from Rhizobiace family, is a major trait in these bacteria required for early steps of plant colonization.


  • Organizational Affiliation

    UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, F-69622, Villeurbanne, Lyon, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic alpha-galactoside-binding protein
A, B, C, D
683Agrobacterium tumefaciensMutation(s): 0 
Gene Names: SY94_4618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose
E, F, G, H
3N/A
Glycosylation Resources
GlyTouCan:  G40178VU
GlyCosmos:  G40178VU
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
RC [auth C],
TD [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth C]
AE [auth D]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth C],
AE [auth D],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth C],
BE [auth D],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth C],
CE [auth D],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth C],
DE [auth D],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth C],
EE [auth D],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth C],
FE [auth D],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth C],
GE [auth D],
HA [auth A],
HB [auth B],
HC [auth B],
HD [auth C],
IA [auth A],
IB [auth B],
IC [auth B],
ID [auth C],
JA [auth A],
JB [auth B],
JC [auth B],
JD [auth C],
K [auth A],
KA [auth A],
KB [auth B],
KC [auth B],
KD [auth C],
L [auth A],
LA [auth A],
LB [auth B],
LC [auth B],
LD [auth C],
M [auth A],
MA [auth A],
MB [auth B],
MC [auth B],
MD [auth C],
N [auth A],
NA [auth A],
NB [auth B],
NC [auth B],
ND [auth C],
O [auth A],
OA [auth A],
OB [auth B],
OC [auth B],
OD [auth C],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth B],
PD [auth C],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
QD [auth C],
R [auth A],
RA [auth A],
RB [auth B],
RD [auth C],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth C],
SD [auth C],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth C],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth C],
UD [auth D],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth C],
VD [auth D],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth C],
WD [auth D],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth C],
XD [auth D],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth C],
YD [auth D],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth C],
ZD [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 354.3α = 90
b = 74.27β = 105.5
c = 108.22γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CNRSFranceMI

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-06-06
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary